The RNA Centric Annotation System Analysis Report

Dilmurat Yusuf, Bora Uyar, Altuna Akalin

About RCAS

RCAS is an RNA-centric annotation system for peaks discovered by CLIP-based high-throughput sequencing methods. The annotation pipeline takes as input a 'bed' format file that contains the genomic coordinates of peak regions. These peaks are overlaid with genomic features that are publicly available (or provided by the user) for the corresponding species. Then, an html based report is generated including figures and graphics that summarize the annotations associated to the peak regions.

GO term enrichment analysis

RCAS calculates GO term enrichment according to the overlap of peak regions in your input file

Gene Set Enrichment Analysis

RCAS calculates enriched sets of genes that overlap with PAR-CLIP peaks from the input BED file

1 Summary Figures

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1.1 Distribution of intervals across gene features

1.2 Distribution of intervals across gene features

1.3 Distribution of intervals across RNA genes

1.4 Distribution of intervals in the genome grouped by gene types

1.5 Distribution of intervals across the chromosomes grouped by gene features

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1.6 Interactive table of genes that overlap peaks

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2 Peak Coverage Profiles

2.1 Coverage of Peak regions across the length of transcripts

2.2 Coverage of Peak regions across the length of Exons

2.3 Coverage of Peak regions across the length of UTRs

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3 GO term and Pathway Enrichment Results

3.1 GO Term Enrichment Results for Biological Processes

3.2 GO Term Enrichment Results for Molecular Functions

3.3 GO Term Enrichment Results for Cellular Compartments

3.4 Gene Set Enrichment Results based on MSigDB

4 TOP MEME motifs discovered in the peak regions

MOTIF 1 MEME width = 8 sites = 517 llr = 2914 E-value = 4.1e-103

MOTIF 2 MEME width = 8 sites = 108 llr = 897 E-value = 7.0e-035

MOTIF 3 MEME width = 8 sites = 38 llr = 342 E-value = 1.9e+004